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| Status |
Public on Jun 05, 2024 |
| Title |
Modifications in the T arm of tRNA globally determine tRNA function and cellular fitness |
| Organism |
Escherichia coli |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
All elongator tRNAs harbor 5-methyluridine at position 54 and pseudouridine at position 55 in the T arm, which are generated by the enzymes TrmA and TruB, respectively. Escherichia coli TrmA and TruB have both been shown to act as tRNA chaperones, and strains lacking trmA or truB are outcompeted by wildtype. Here, we investigate how TrmA and TruB contribute to cellular fitness. Deletion of trmA and truB in E. coli causes a global decrease in aminoacylation and alters other tRNA modification such as acp3U47 and 4-thiouridine. Whereas global protein synthesis is not significantly changed in ΔtrmA and ΔtruB, the expression of many specific proteins is altered at the translational level. In conclusion, we demonstrate that universal modifications of the tRNA T arm are critical for global tRNA function by enhancing other tRNA modifications, tRNA folding, tRNA aminoacylation, and translation of specific genes thereby improving cellular fitness and explaining their conservation.
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| Overall design |
To examine how mRNA levels compare between Escherichia coli lacking trmA, truB, or both trmA and truB genes and the parental E. coli BW25113 strain, we extracted total RNA from each strain after growth in LB + 2% sodium formate to an OD600 between 0.3 and 0.4 using TRIzol. Three biological replicates were performed for each strain.
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| Contributor(s) |
Schultz SK, Katanski CD, Fahlman R, Pan T, Kothe U |
| Citation(s) |
38889150 |
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| Submission date |
Jul 18, 2023 |
| Last update date |
Sep 05, 2024 |
| Contact name |
Ute Kothe |
| E-mail(s) |
ute.kothe@umanitoba.ca
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| Organization name |
University of Manitoba
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| Department |
Chemistry
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| Street address |
144 Dysart Road
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| City |
Winnipeg |
| State/province |
MB |
| ZIP/Postal code |
R3T 2N2 |
| Country |
Canada |
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| Platforms (1) |
| GPL21433 |
Illumina HiSeq 4000 (Escherichia coli) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA996030 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE237609_RAW.tar |
800.0 Kb |
(http)(custom) |
TAR (of TXT) |
| GSE237609_diff_exp_analysis_WT-trmA-truB.csv.gz |
275.0 Kb |
(ftp)(http) |
CSV |
| GSE237609_diff_exp_analysis_WT-trmA.csv.gz |
261.2 Kb |
(ftp)(http) |
CSV |
| GSE237609_diff_exp_analysis_WT-truB.csv.gz |
269.1 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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